<?xml version="1.0"?>
<tool id="mentalist_build" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.2">
  <requirements>
    <requirement type="package" version="0.1.2">mentalist</requirement>
  </requirements>
  <command detect_errors="exit_code">
  <![CDATA[
	   mkdir mentalist-database && cd mentalist-database &&
	   MentaLiST.jl
	   build_db
	   --db '$kmer_database'
	   -k '$kmer_size'
	   #if $profile
	   -p '$profile'
	   #end if
	   -f ${" ".join(map(str, $input_fastas))} &&
	   cd .. &&
	   python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
  ]]>
  </command>
  <inputs>
    <param name="kmer_size" type="integer"
	   label="Kmer size" help="Kmer size"
	   value="31" min="1" max="32" />
    <param name="input_fastas" type="data_collection" collection_type="list" format="fasta" multiple="true"
	   label="Input Fasta" help="Fasta input files" />
    <param name="profile" type="data" format="tsv" optional="true"
	   label="Profile" help="Profile for known genotypes" />
  </inputs>
  <outputs>
    <data name="out_file" format="data_manager_json" />
  </outputs>
  <citations>
    <citation type="doi">10.1101/172858</citation>
  </citations>
</tool>